Despite fears of violence the duel between President Yoweri Museveni and Opposition leader, Kizza Besigye, the most serious challenger to Museveni’s 20 year rule, went ahead peacefully.
Election officials reported no serious problems and foreign poll monitors said their most troubling findings had been unsealed ballot boxes and voters being turned away when their names were not found in registries.
The extent of such incidences was not immediately clear although thousands of people were left standing in line at the official close of voting.
However Opposition leader, Dr Besigye, and his Forum for Democratic Change (FDC) accused the ruling National Resistance Movement (NRM) of intimidation through massive security deployments and complained of widespread irregularities.
"This was an appalling exercise," FDC spokesman Sam Akaki told AFP, insisting at the same time that Dr Besigye, President Museveni's main rival, would win.
But NRM spokesman Ofwono Opondo said the vote had been "peaceful, very democratic, free and fair" and accused the FDC of being "bad losers," maintaining that President Museveni would coast to victory.
Counting began immediately after the close at those of the nearly 19,000 stations.
Very preliminary partial returns gave Besigye a slight lead in Kampala but showed Museveni well ahead in the countryside.
Final results are due on Saturday and while observers said it was too early to say if the election had met international standards, they expressed relative satisfaction with the process.
"We'll have to wait and see, but the country is calm and it seems people have picked up the idea that there is a choice between change and continuity," Max Van Der Berg, chief of the European Union observer mission, told AFP.
About 10.4 million Ugandans were eligible to vote for one of five presidential candidates and the 310-member parliament but the campaign was overshadowed by the main contenders in the race for the top job.